View Compound Workbench

The Periodic Table in Catalyst

Introduction

When you first open a View Compound workbench, a compact version of the Periodic Table appears at the top right corner of the screen. While you are building a molecule, you can use the Periodic Table to:

Select an element.
Select a substituent.

If you close the View Compound workbench, the Periodic Table remains open. It stays on the screen until you exit from Catalyst.

You can view the Periodic Table either in its initial compact form or in its full version. The compact version shows the eleven elements most commonly-used in medicinal chemistry.

To expand the compact version of the table to the full version, click the expansion button at the left side of the contracted table.

To shrink the full version of the table back to the contracted form, click the shrink button at the bottom left corner of the full table.

Selecting elements from the table

Use the Periodic Table in the View Compound workbench to specify what element to use next time you add or change an atom in the 2D or 3D workspace.

For example, if you want to add an oxygen atom to your molecule, make sure nothing is selected in the workspace, then click O in the Periodic Table, and place a new atom in either workspace. The O button remains selected.

If you want to change an existing atom to an oxygen, extend-select (middle button) the desired atom in the workspace, then click O in the Periodic Table. You can also use keyboard shortcuts for selecting common elements.

If you work in a lab or in a different workbench, you then need to click an object or button in the View Compound workbench before you can select another atom or substituent from the Periodic Table.

For more information on adding atoms, see To add atoms and substituents.

For more information on changing atoms, see To change atoms to other elements or substituents.

Selecting substituents from the table

You can use the menus on the menu bar at the bottom of the Periodic Table to select substituents to add to your molecule in the workbench.

For example, to add a cyclohexyl group, select the Rings/Cyclohexyl menu item.

When you select a substituent, it becomes the currently active choice, and its name appears at the right side of the compact Periodic Table or at the top of the full Periodic Table.

See To change molecular topology for more information on adding substituents.

See Building peptides for details on how to use the Amino Acids menu to build peptides.

Building peptides

You can use amino acid building blocks provided by the Amino Acids menu in the Periodic Table to build peptides and proteins from N-terminus to C-terminus. When you add an amino acid with this menu, it appears in the workspace as an aldehyde rather than as an acid. This makes it easier to build peptides, since a new amino acid can be added to one already in the workspace by eliminating the aldehydic hydrogen to form the peptide link.

To build peptides:

Open the View Compound workbench.
Make sure the workspace is clear (select the Edit/Clear Display menu item, if necessary).
Select an amino acid from the Amino Acids menu in the Periodic Table.
Click in either workspace. The selected amino acid appears in its aldehydic form.
Click the Deselect button in the toolbox to deselect everything. Use extend-select in either workspace to select the aldehydic hydrogen that is to be eliminated to form the peptide link.
From the Amino Acids menu in the Periodic Table, select the next amino acid to add. The selected hydrogen in the workspace is replaced by the chosen amino acid. A peptide link appears between the carbonyl carbon on the existing amino acid and the nitrogen on the newly-added amino acid.
Repeat Steps 4 and 5 to add additional amino acids to the peptide.
You may find it helpful to periodically use the Tools/2D Beautify and Tools/Generate Standard 3D menu items to clean up the 2D and 3D molecules as you build the amino acid.
When you have finished adding amino acids, you need to convert the aldehydic hydrogen at the C terminus to an oxygen to obtain an acid terminus.
Select the aldehydic hydrogen at the C terminus.
Select O in the Periodic Table.
The selected hydrogen is replaced by an oxygen.
Save your peptide to the shelf when you have finished building it.

Here is an example of a peptide made by placing cysteinyl, then adding phenylalanyl, and then alanyl:

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